EMD-9316

Single-particle
6.35 Å
EMD-9316
3D View Gallery
Deposition: 10/11/2018
Map released: 05/12/2018
Last modified: 20/03/2024
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EMD-9316
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Dihedral oligomeric complex of GyrA N-terminal fragment with DNA, solved by cryoEM in C2 symmetry

EMD-9316

Single-particle
6.35 Å
EMD-9316
3D View Gallery
Deposition: 10/11/2018
Map released: 05/12/2018
Last modified: 20/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.5
Buffer components [3]:
Name Formula Concentration ChEBI
Tris - 50.0 mM -
Potassium chloride KCl 55.0 mM
Strontium chloride SrCl2 10.0 mM
Grid
Mesh: 400
Model: C-flat-1.2/1.3 4C
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON - -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 277 K
Instrument: FEI VITROBOT MARK IV
Microscopy [1]
Microscope: JEOL 3200FS
Illumination mode: OTHER
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 50.0 µm
Nominal CS: 2.0 mm
Nominal defocus: 1.0 µm - 3.0 µm
Nominal magnification: 30000.0
Calibrated magnification: 40323.0
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Temperature
Minimum: 100.0 K
Maximum: 100.0 K
Specialist optics
Energy filter
Name: In-column Omega Filter
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: COUNTING
Dimensions: 3710 pixel x 3838 pixel
Frames per image: 1-40
Number of real images: 718
Average exposure time: 12.0 s
Average electron dose per image: 62.0 e/Å2
Image processing [1]
Final reconstruction
Resolution: 6.35 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 30637
Algorithm: FOURIER SPACE
⌯ Applied Symmetry
Point group: C2
Software [1]
Name Version Details
RELION 2.1 -
Startup model [1]
Type: OTHER
Details:Back projection from 3 orthogonal views
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 1.4 -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
RELION 2.1 -
Particle selection [1]
Selected Ref. model Method Software Details
387297 - - - -
Final 3D classification
Number of classes: 4
Software [1]
Name Version Details
RELION 2.1 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Dihedral oligomeric complex of GyrA N-terminal fragment with DNA, solved by cryoEM in C2 symmetry
⬡ Geometry
X Y Z
Dimensions 200 200 200
Origin 0 0 0
Spacing 200 200 200
Voxel size 1.24 Å 1.24 Å 1.24 Å
Contour list
Primary Level Source
True 0.059 AUTHOR